Variant report

Variant	rs539244
Chromosome Location	chr12:57877863-57877864
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Distal block	Cell Line	Cell type
1	chr12:57872773..57878513-chr12:57879040..57886839,8	K562	blood:
2	chr12:57865716..57868147-chr12:57875960..57878891,2	K562	blood:
3	chr12:57869469..57872430-chr12:57877374..57879716,2	K562	blood:

Variant related genes	Relation type
ENSG00000123329	Chromatin interaction
ENSG00000166986	Chromatin interaction

Extended variants
information (count: 29 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:13)

rs_ID	r²[population]
rs1284606	0.80[AMR][1000 genomes];0.92[EUR][1000 genomes]
rs1617196	0.81[AMR][1000 genomes];0.97[EUR][1000 genomes]
rs1709874	0.80[ASN][1000 genomes]
rs2672571	0.91[EUR][1000 genomes];0.90[ASN][1000 genomes]
rs472895	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs508904	0.91[AFR][1000 genomes];0.82[AMR][1000 genomes];0.92[EUR][1000 genomes];0.89[ASN][1000 genomes]
rs511752	0.80[AMR][1000 genomes];0.94[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs541869	0.86[AMR][1000 genomes];0.94[EUR][1000 genomes];0.99[ASN][1000 genomes]
rs542278	0.80[AFR][1000 genomes];0.83[AMR][1000 genomes];0.91[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs569251	0.89[AFR][1000 genomes];0.88[AMR][1000 genomes];0.92[EUR][1000 genomes];0.98[ASN][1000 genomes]
rs776038	0.80[ASN][1000 genomes]
rs796546	0.80[ASN][1000 genomes]
rs899653	0.90[EUR][1000 genomes];0.90[ASN][1000 genomes]

Variant overlapped rSNPs/rCNVs (count:16 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv1046013	chr12:57714676-57895167	Active TSS Enhancers Bivalent Enhancer Genic enhancers Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
2	nsv541502	chr12:57714676-57895167	Weak transcription Flanking Bivalent TSS/Enh Strong transcription Flanking Active TSS Active TSS Genic enhancers Bivalent Enhancer Enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA	56 gene(s)	inside rSNPs	diseases
3	nsv899117	chr12:57811414-57926472	Enhancers Active TSS Flanking Active TSS Weak transcription Strong transcription Genic enhancers Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh Bivalent/Poised TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	103 gene(s)	inside rSNPs	diseases
4	nsv899118	chr12:57811414-57946477	Weak transcription Strong transcription Flanking Active TSS Enhancers Flanking Bivalent TSS/Enh Genic enhancers Active TSS Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	106 gene(s)	inside rSNPs	diseases
5	esv1812398	chr12:57829733-58001868	Flanking Active TSS Active TSS Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Weak transcription Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
6	esv2758310	chr12:57829733-58001868	Active TSS Genic enhancers Enhancers Weak transcription Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
7	esv2759901	chr12:57829733-58001868	Enhancers Flanking Bivalent TSS/Enh Flanking Active TSS Bivalent Enhancer Active TSS Weak transcription Strong transcription Transcr. at gene 5' and 3' Bivalent/Poised TSS Genic enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
8	nsv428283	chr12:57829733-58001868	Flanking Active TSS Active TSS Transcr. at gene 5' and 3' Strong transcription Flanking Bivalent TSS/Enh Weak transcription Enhancers Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	96 gene(s)	inside rSNPs	diseases
9	nsv469411	chr12:57844049-57921188	Active TSS Flanking Active TSS Strong transcription Weak transcription Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
10	nsv559032	chr12:57844049-57921188	Enhancers Flanking Active TSS Flanking Bivalent TSS/Enh Weak transcription Bivalent/Poised TSS Active TSS Strong transcription Transcr. at gene 5' and 3' Genic enhancers Bivalent Enhancer ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
11	nsv559033	chr12:57848639-57946477	Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Strong transcription Genic enhancers Bivalent/Poised TSS Enhancers ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	92 gene(s)	inside rSNPs	diseases
12	nsv899119	chr12:57851182-57923451	Strong transcription Flanking Active TSS Active TSS Weak transcription Enhancers Genic enhancers Transcr. at gene 5' and 3' Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
13	nsv559034	chr12:57859932-58012233	Strong transcription Weak transcription Flanking Active TSS Enhancers Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Active TSS ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	89 gene(s)	inside rSNPs	diseases
14	nsv819781	chr12:57873564-57882217	Weak transcription Active TSS Flanking Active TSS Enhancers Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	17 gene(s)	inside rSNPs	n/a
15	nsv1038741	chr12:57877355-58174506	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases
16	nsv541503	chr12:57877355-58174506	Enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Weak transcription Active TSS Bivalent/Poised TSS Genic enhancers Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA miRNA target site	126 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs539244	DCTN2	cis	Muscle Skeletal	GTEx

Chromatin state (count:53 , 50 per page) page: 1 2

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr12:57871600-57881200	Weak transcription	ES-UCSF4 Cell Line	embryonic stem cell
2	chr12:57871600-57881200	Weak transcription	Right Atrium	heart
3	chr12:57873200-57881200	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
4	chr12:57873600-57881000	Weak transcription	Dnd41	blood
5	chr12:57874000-57881200	Weak transcription	Thymus	Thymus
6	chr12:57874600-57881000	Weak transcription	Spleen	Spleen
7	chr12:57875000-57881200	Weak transcription	Primary T helper 17 cells PMA-I stimulated	--
8	chr12:57875600-57881000	Weak transcription	Primary T killer memory cells from peripheral blood	blood
9	chr12:57875800-57881000	Weak transcription	Primary T cells fromperipheralblood	blood
10	chr12:57875800-57881000	Weak transcription	Primary Natural Killer cells fromperipheralblood	blood
11	chr12:57875800-57881000	Weak transcription	Primary T killer naive cells fromperipheralblood	blood
12	chr12:57875800-57881000	Weak transcription	K562	blood
13	chr12:57875800-57881200	Weak transcription	Primary T cells from cord blood	blood
14	chr12:57875800-57881200	Weak transcription	Primary T helper memory cells from peripheral blood 2	blood
15	chr12:57875800-57881200	Weak transcription	Primary T helper naive cells fromperipheralblood	blood
16	chr12:57875800-57881200	Weak transcription	Primary T cells effector/memory enriched fromperipheralblood	blood
17	chr12:57875800-57881200	Weak transcription	Fetal Thymus	thymus
18	chr12:57875800-57881400	Weak transcription	H1 Cell Line	embryonic stem cell
19	chr12:57876000-57881000	Weak transcription	Primary T helper naive cells from peripheral blood	blood
20	chr12:57876000-57881200	Weak transcription	Primary neutrophils fromperipheralblood	blood
21	chr12:57876000-57881200	Weak transcription	Primary hematopoietic stem cells	blood
22	chr12:57876000-57881200	Weak transcription	Primary hematopoietic stem cells short term culture	blood
23	chr12:57876000-57881200	Weak transcription	Primary T regulatory cells fromperipheralblood	blood
24	chr12:57876000-57881200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Male	--
25	chr12:57876000-57881200	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
26	chr12:57876200-57881200	Weak transcription	Primary hematopoietic stem cells G-CSF-mobilized Female	--
27	chr12:57876800-57881000	Weak transcription	Primary T helper cells fromperipheralblood	blood
28	chr12:57877200-57878400	Enhancers	Primary B cells from peripheral blood	blood
29	chr12:57877400-57881000	Weak transcription	Primary T helper cells PMA-I stimulated	--
30	chr12:57877400-57881200	Weak transcription	HUES48 Cell Line	embryonic stem cell
31	chr12:57877400-57881200	Weak transcription	Adipose Derived Mesenchymal Stem Cell Cultured Cells	ES cell derived
32	chr12:57877400-57881200	Weak transcription	Fetal Kidney	kidney
33	chr12:57877400-57881200	Weak transcription	NHLF	lung
34	chr12:57877400-57881400	Weak transcription	HUES64 Cell Line	embryonic stem cell
35	chr12:57877600-57878800	Weak transcription	iPS-20b Cell Line	embryonic stem cell
36	chr12:57877600-57879200	Weak transcription	ES-I3 Cell Line	embryonic stem cell
37	chr12:57877600-57879200	Weak transcription	iPS-18 Cell Line	embryonic stem cell
38	chr12:57877600-57881000	Weak transcription	GM12878-XiMat	blood
39	chr12:57877600-57881000	Weak transcription	HSMMtube	muscle
40	chr12:57877600-57881200	Weak transcription	HUES6 Cell Line	embryonic stem cell
41	chr12:57877600-57881200	Weak transcription	Bone Marrow Derived Cultured Mesenchymal Stem Cells	Bone marrow
42	chr12:57877600-57881200	Weak transcription	Muscle Satellite Cultured Cells	--
43	chr12:57877600-57881200	Weak transcription	Foreskin Melanocyte Primary Cells skin01	Skin
44	chr12:57877600-57881200	Weak transcription	HSMM	muscle
45	chr12:57877600-57881200	Weak transcription	NH-A	brain
46	chr12:57877600-57881400	Weak transcription	H9 Cell Line	embryonic stem cell
47	chr12:57877600-57881400	Weak transcription	H9 Derived Neuronal Progenitor Cultured Cells	ES cell derived
48	chr12:57877600-57881400	Weak transcription	iPS-15b Cell Line	embryonic stem cell
49	chr12:57877600-57881800	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
50	chr12:57877800-57881200	Weak transcription	IMR90 fetal lung fibroblasts Cell Line	lung

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